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Molecular insights into capsular polysaccharide secretion. Kuklewicz J, Zimmer J. Nature. 2024 Apr 25;628(8009):901–909.

Mechanical activation opens a lipid-lined pore in OSCA ion channels. Han Y, Zhou Z et al. Nature. 2024 Apr 25;628(8009):910–918.

Bitter taste receptor activation by cholesterol and an intracellular tastant. Kim Y, Gumpper RH et al. Nature. 2024 Apr 18;628(8008):664–671.

Structure and assembly of a bacterial gasdermin pore. Johnson AG, Mayer ML et al. Nature. 2024 Apr 18;628(8008):657–663.

Structural basis of DNA crossover capture by Escherichia coli DNA gyrase. Vayssières M, Marechal N et al. Science. 2024 Apr 12;384(6692):227-232.

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News

January 22, 2024

ChimeraX 1.7.1 is available, with fixes for a few miscellaneous bugs that were identified after the 1.7 release.

December 19, 2023

The ChimeraX 1.7 production release is available! See the change log for what's new. Future Mac releases will require macOS 11 or higher.

November 6, 2023

The ChimeraX 1.7 release candidate is available – please try it and report any issues. See the change log for what's new.

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UCSF ChimeraX

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and personal use. Commercial users, please see ChimeraX commercial licensing.

ChimeraX is developed with support from National Institutes of Health R01-GM129325, Chan Zuckerberg Initiative grant EOSS4-0000000439, and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases.

Feature Highlight

THRβ and binding-site rotamers rotamer list dialog

Rotamers and Swapaa Virtual Mutation

Rotamers is an interface for showing amino acid sidechain rotamers and optionally replacing the original sidechain, also implemented as the swapaa command. The rotamers can be shown all at once, as in the figure, or individually by choosing rows in the dialog.

The figure shows binding-site residues of the thyroid hormone receptor β with hormone bound, PDB 3gws. Rotamers for the hormone-resistance mutations N331H and L346R are shown as partially transparent sticks, with H-bonds (light blue dashed line) and clashes (light purple dashed lines) calculated for the histidine rotamers at position 331. The rotamer-list dialog for this position is also shown. Command script rotamers.cxc contains the initial, noninteractive part of the setup.

These mutations are described in Cardoso et al., Endocrine (2020). Although one histidine rotamer may be able to form the same pocket-stabilizing H-bond as the wild-type asparagine, it also clashes with several atoms (third row in the dialog). H-bonds and clashes are not shown for the arginine rotamers at 346, but they all clash significantly with the hormone and/or other pocket atoms.

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Example Image

HIV-1 protease B-factor coloring

B-factor Coloring

Atomic B-factor values are read from PDB and mmCIF input files and assigned as attributes that can be shown with coloring and used in atom specification. This example shows B-factor variation within a structure of the HIV-1 protease bound to an inhibitor (PDB 4hvp). For complete image setup, including positioning, color key, and label, see the command file bfactor.cxc.

Additional color key examples can be found in tutorials: Coloring by Electrostatic Potential, Coloring by Sequence Conservation

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